Table 5_Integrated transcriptomic and metabolomic analysis reveals the molecular mechanisms underlying wheat germinating seed response to exogenous abscisic acid stress.xlsx

IntroductionPhytohormone abscisic acid (ABA) plays a pivotal regulatory role in crop responses to abiotic stress. However, the specificities of the coordinated transcriptional and metabolic regulatory network in wheat under ABA signaling remain to be fully elucidated.
MethodsThis study systematically investigated the regulatory effects of exogenous ABA on wheat germinating seeds through integrated physiological, transcriptomic, and metabolomic analyses.
ResultsPhysiological results demonstrated that low-concentration ABA (2 mg·L-1) promoted primary root elongation (12% increase vs. 0 mg·L-1 (CK)), whereas high concentrations (≥4 mg·L-1) significantly inhibited growth (40% root length reduction under 6 mg·L-1 ABA). Concurrently, electrolyte leakage, malondialdehyde (MDA) content, and catalase (CAT) activity markedly increased with ABA concentration (P < 0.05), indicating aggravated oxidative stress. Transcriptomic profiling (CK vs. 6 mg·L-1 ABA) identified 854 differentially expressed genes (DEGs; 470 up-regulated/384 down-regulated). Gene Ontology (GO) enrichment revealed DEGs predominantly involved in “Cellular process”, “Metabolic process”, “Catalytic activity”, and “Transporter activity”. KEGG analysis highlighted activation of “Linoleic acid metabolism”, “Alpha-Linolenic acid metabolism”, “Glycolysis/Gluconeogenesis”, and “Biosynthesis of amino acids” pathways. Metabolomics detected 665 differentially accumulated metabolites (DAMs), with “Lipids”, “Organic acids”, and “Amino acids” exhibiting significant alterations. KEGG enrichment emphasized “benzoxazinoid biosynthesis” and “Nicotinate/nicotinamide metabolism”. Integrative multi-omics analysis uncovered 10 core pathways, such as “Glycolysis/Gluconeogenesis”, “Biosynthesis of amino acids”, and “Cysteine and methionine metabolism”, that orchestrating ABA stress responses. Notably, L-serine and the genes TraesCS3A02G276100 and TraesCS5A02G398300 were recurrently implicated in multiple pathways, indicating their function as key network nodes.
DiscussionThis study elucidates the molecular mechanisms by which wheat adapts to ABA stress through dynamic reprogramming of its metabolic and gene expression networks, thereby laying a theoretical foundation for developing future ABA-based seed treatment technologies or stress-resistant breeding strategies.

引言
植物激素脱落酸（abscisic acid, ABA）在作物响应非生物胁迫过程中发挥关键调控作用。然而，小麦在脱落酸信号通路下协同转录与代谢调控网络的具体作用机制仍有待全面阐明。

方法
本研究通过整合生理学、转录组学与代谢组学分析，系统探究了外源脱落酸对小麦萌发种子的调控效应。

结果
生理学实验结果显示，低浓度脱落酸（2 mg·L⁻¹）可促进小麦初生根伸长（较0 mg·L⁻¹对照（CK）提升12%），而高浓度（≥4 mg·L⁻¹）则显著抑制生长（6 mg·L⁻¹脱落酸处理下根长缩短40%）。与此同时，电解质渗漏率、丙二醛（malondialdehyde, MDA）含量与过氧化氢酶（catalase, CAT）活性均随脱落酸浓度升高显著上升（P < 0.05），表明氧化胁迫加剧。转录组分析（CK vs 6 mg·L⁻¹脱落酸处理组）共鉴定出854个差异表达基因（differentially expressed genes, DEGs），其中上调基因470个、下调基因384个。基因本体（Gene Ontology, GO）富集分析显示，差异表达基因主要富集于“细胞过程（Cellular process）”“代谢过程（Metabolic process）”“催化活性（Catalytic activity）”及“转运蛋白活性（Transporter activity）”条目。KEGG通路分析显示，亚油酸代谢（Linoleic acid metabolism）、α-亚麻酸代谢（Alpha-Linolenic acid metabolism）、糖酵解/糖异生（Glycolysis/Gluconeogenesis）及氨基酸生物合成（Biosynthesis of amino acids）通路被显著激活。代谢组学共鉴定出665个差异累积代谢物（differentially accumulated metabolites, DAMs），其中脂质（Lipids）、有机酸（Organic acids）及氨基酸（Amino acids）类代谢物发生显著变化。KEGG富集分析进一步凸显了苯并恶嗪类生物合成（benzoxazinoid biosynthesis）及烟酸/烟酰胺代谢（Nicotinate/nicotinamide metabolism）通路的重要性。整合多组学分析共筛选出10条核心调控通路，包括糖酵解/糖异生、氨基酸生物合成及半胱氨酸和甲硫氨酸代谢（Cysteine and methionine metabolism）等，这些通路共同调控脱落酸胁迫响应。值得注意的是，L-丝氨酸及TraesCS3A02G276100、TraesCS5A02G398300这两个基因反复出现在多条通路中，表明它们作为关键网络节点发挥功能。

讨论
本研究通过解析小麦代谢与基因表达网络的动态重编程过程，阐明了其适应脱落酸胁迫的分子机制，为未来开发基于脱落酸的种子处理技术或抗逆育种策略奠定了理论基础。